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Plot Abundance Profile

Source: R/plot-featureprofile.R
plot_abundanceprofile.Rd

Creates a profile plot showing the abundance distribution of features across different classes.

Usage

plot_abundanceprofile(
  data,
  variable,
  qc_types,
  log_scale,
  use_qc_metrics = FALSE,
  feature_map = NA,
  show_sum = NA,
  exclude_classes = NA,
  filter_data = FALSE,
  include_qualifier = FALSE,
  include_istd = FALSE,
  include_feature_filter = NA,
  exclude_feature_filter = NA,
  analysis_range = NA,
  drop_empty_classes = TRUE,
  density_strip = FALSE,
  scale_factor = 1,
  x_lim = NA,
  x_label = NA,
  y_axis_position = "right",
  segment_width = 0.25,
  font_base_size = 8,
  grid_major_color = "grey50",
  grid_major_linewidth = 0.1,
  grid_minor_color = "grey50",
  grid_minor_linewidth = 0.1
)

Arguments

data

A MRMhubExperiment object.

variable

A character string indicating the variable to plot. For use_qc_metrics = FALSE, this must be a base name like "area" or "conc". For use_qc_metrics = TRUE, this is the base name of a metric in the metrics_qc table (e.g., "rt" for "rt_mean_SPL").

qc_types

A character vector specifying the QC types to be averaged and plotted. If use_qc_metrics is TRUE, this must be a single character string (e.g., "SPL").

log_scale

A logical value indicating whether to use a log10 scale for the x-axis.

use_qc_metrics

A logical value. If FALSE (default), data is summarized on the fly from the main dataset. If TRUE, pre-calculated summary data is used from the metrics_qc table, which is much faster. When TRUE, qc_types must specify only one QC type.

feature_map

A named character vector specifying feature classes, their order, and color. The order of the vector determines the y-axis order. Alternatively, can be a single string: lipidomics to use a default theme comprising mapping for lipid classes frequently measured in lipidomics methods. When using the default theme, set drop_empty_classes = TRUE to avoid showing classes not present in the data. If NA (default), the default theme is used.

show_sum

A logical value indicating whether to plot a summary point (diamond shape) representing the mean of the summed abundances for each class. Defaults to TRUE for abundance-related variables and FALSE for others (e.g., "rt", "fwhm").

exclude_classes

A character vector of feature classes to be excluded from the plot.

filter_data

A logical value indicating whether to use all data (FALSE, default) or only QC-filtered data (TRUE, via filter_features_qc()). This is ignored if use_qc_metrics is TRUE.

include_qualifier

A logical value indicating whether to include qualifier features. Default is FALSE.

include_istd

A logical value indicating whether to include internal standard (ISTD) features. Default is FALSE.

include_feature_filter

A character or regex pattern to filter features by feature_id. If a vector is supplied, features matching any pattern will be included.

exclude_feature_filter

A character or regex pattern to exclude features by feature_id. If a vector is supplied, features matching any pattern will be excluded.

analysis_range

A numeric vector of length 2 specifying the inclusive range of analysis_order. If NA (default), all analyses are included.

drop_empty_classes

A logical value. If TRUE (default), feature classes from feature_map that are not found in the data are removed from the plot. If FALSE, they are kept as empty rows.

density_strip

A logical value. If TRUE, a density strip showing the distribution of all features is added to the top of the plot.

scale_factor

A numeric value to scale the selected variable. Default is 1.

x_lim

A numeric vector of length 2 specifying the x-axis limits. If log_scale is TRUE, these are interpreted as exponents (e.g., c(2, 6) for 10^2 to 10^6). If NA, limits are determined automatically from the data.

x_label

A character string for the x-axis label. If NA, a default label is generated.

y_axis_position

A character string specifying the y-axis position ("left" or "right"). Default is "right".

segment_width

A numeric value for the linewidth of the feature segments. Default is 0.25.

font_base_size

A numeric value for the base font size. Default is 8.

grid_major_color

Color for major grid lines. Default is "grey50".

grid_major_linewidth

Linewidth for major grid lines. Default is 0.1.

grid_minor_color

Color for minor grid lines. Default is "grey50".

grid_minor_linewidth

Linewidth for minor grid lines. Default is 0.1.

Value

A ggplot object representing the abundance profile plot.